GNNAS-Dock: Budget Aware Algorithm Selection with Graph Neural Networks for Molecular Docking

Molecular docking is a major element in drug discovery and design. It enables the prediction of ligand-protein interactions by simulating the binding of small molecules to proteins. Despite the availability of numerous docking algorithms, there is no single algorithm consistently outperforms the others across a diverse set of docking scenarios. This paper introduces GNNAS-Dock, a novel Graph Neural Network (GNN)-based automated algorithm selection system for molecular docking in blind docking situations. GNNs are accommodated to process the complex structural data of both ligands and proteins. They benefit from the inherent graph-like properties to predict the performance of various docking algorithms under different conditions. The present study pursues two main objectives: 1) predict the performance of each candidate docking algorithm, in terms of Root Mean Square Deviation (RMSD), thereby identifying the most accurate method for specific scenarios; and 2) choose the best computationally efficient docking algorithm for each docking case, aiming to reduce the time required for docking while maintaining high accuracy. We validate our approach on PDBBind 2020 refined set, which contains about 5,300 pairs of protein-ligand complexes.

A case study of algorithm selection for the traveling thief problem

Many real-world problems are composed of several interacting components. In order to facilitate research on such interactions, the Traveling Thief Problem (TTP) was created in 2013 as the combination of two well-understood combinatorial optimization problems. With this article, we contribute in four ways. First, we create a comprehensive dataset that comprises the performance data of 21 TTP algorithms on the full original set of 9720 TTP instances. Second, we define 55 characteristics for all TPP instances that can be used to select the best algorithm on a per-instance basis. Third, we use these algorithms and features to construct the first algorithm portfolios for TTP, clearly outperforming the single best algorithm. Finally, we study which algorithms contribute most to this portfolio.